I am new to metabolomics and have never used GC-MS. I am analyzing the common compounds (nothing specific) present in the cell-free supernatant of Lactobacillus, and I do not know if I can submit my sample without further processing. Thank you for any help!
Depends on a lot of factors and what exactly you are looking for. Any sample introduced into GCMS, needs to be thermally stable and also volatilized inorder to be separated on the GC column for efficient identification on the MS. If it is volatiles (VOCs) you are looking for, you may not need any further processing of the samples. If you are looking for lipids, fatty acids, esters and likewise compounds, some sort of pre-processing may be required, like derivitization techniques - acylation, alkylation, silylation, among others.
You need to specify what you are looking for to identify from the beginning of the extraction. In addition to derivatization techniques, you need to consider the best extraction solvent based on polarity of your fraction and the right concentration methods if necessary. The accuracy of your result depends on your sample preparation.
This is a very broad question, which needs to be more specific in order to get to the bottom of it.
First, learning GC-MS. You need to read first about the technique and understand what are the theories and practices that make a GC to be an analytical instrument. Follow that with reading about MS to understand how it is used as a detection instrument to be combined with a GC to make a functional analytical system.
Then you need someone in your university of company or workplace who has hands-on experience with whatever instrument you have available to give you the practical side of the theory, which is the physical instrument, how does it work, how to introduce samples, what kind of detectors it has, etc.
Then yon need to gather information from the literature (mostly published papers or published test methods) about the matrix (sample) that you would like to analyze and the analyte of interest in this matrix that you'd like to detect/quantify. When reading the literature you'll make more sense of what is written there only when you have completed steps 1 and 2 above. Going directly to reading published materials without going through steps 1 and 2 is as useless as getting a passenger on an airplane to try landing the plane safely, it won't happen and it makes no sense at all.
Learning the science of chromatography is a lengthy path that takes years to reach only 40% of the full path. So I strongly advice you to find the right starting point before you get involved in stuff that can't find a place in your mind.
Best luck.
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